The problem is that the pads suck and the rotors are of inferior quality. Jeep finally realized this and started putting a little better pad on the 2001(maybe 2000) and up Grand Cherokees, from what I've heard.
The reason the rotors warp is heat. The pads aren't very good so they build up heat in the rotors. When you come to a stop the rotor cools off at different rates due to a hot pad/caliper next to one part and the rest not being insulated. The different rates of heat dissipation causes warpage.
When you switch to good pads and a set of x-drilled or slotted rotors a couple of things happen.
1) The pads are better, you stop quicker.
2) The rotors are a better quality (if you buy a good set)
3) The slotting (if you go that route) allows gasses built up between the pad and the rotor to bleed off while braking, increasing efficiency/decreasing fade.
4) The x-drilling does the same thing, and it also allows more airflow to cool the rotors.
But if you practice your 100mph-0 stops and stop for a little bit, you're probably going to warp anything. If you haul yourself to a halt quickly you might want to consider rolling forward a foot or two every couple of seconds to rotate the brake rotor, thus allowing a more even cool-down.
But I'm no engineer, what do I know?